Revert "Implement molecular interaction visualization (H-bonds, salt bridges, disulfide bonds)"

This reverts commit 380211a.

Author: AmirMohammad Cheraghali

src/App.tsx

@@ -90,7 +90,6 @@ function App() {
   const [showLigands, setShowLigands] = useState(initialUrlState.showLigands || false);
   const [showIons, setShowIons] = useState(false);
   const [showSurface, setShowSurface] = useState(initialUrlState.showSurface || false);
-  const [showInteractions, setShowInteractions] = useState(false);
 
   // ... (lines 53-343) ...
 
@@ -1001,8 +1000,6 @@ function App() {
             setShowLigands={setShowLigands}
             showIons={showIons}
             setShowIons={setShowIons}
-            showInteractions={showInteractions}
-            setShowInteractions={setShowInteractions}
             onFocusLigands={handleFocusLigands}
             onRecordMovie={handleRecordMovie}
             isRecording={isRecording}
@@ -1053,7 +1050,6 @@ function App() {
         showSurface={showSurface}
         showLigands={showLigands}
         showIons={showIons}
-        showInteractions={showInteractions}
         coloring={coloring}
         palette={colorPalette}
         backgroundColor={customBackgroundColor || (isLightMode ? 'white' : 'black')}

src/components/Controls.tsx

@@ -288,8 +288,6 @@ interface ControlsProps {
     setShowSurface: (show: boolean) => void;
     showLigands: boolean;
     setShowLigands: (show: boolean) => void;
-    showInteractions: boolean;
-    setShowInteractions: (show: boolean) => void;
     onFocusLigands: () => void;
     onRecordMovie: (duration: number) => void;
     isRecording: boolean;
@@ -356,8 +354,6 @@ export const Controls: React.FC<ControlsProps> = ({
     setShowLigands,
     showIons,
     setShowIons,
-    showInteractions,
-    setShowInteractions,
     onRecordMovie,
     isRecording,
     proteinTitle,
@@ -1199,20 +1195,6 @@ export const Controls: React.FC<ControlsProps> = ({
                                             <span className={`w-1.5 h-1.5 rounded-full ${showIons ? 'bg-purple-500' : 'bg-neutral-400'}`} />
                                             {showIons ? 'Ions On' : 'Ions Off'}
                                         </button>
-                                        {!isChemical && (
-                                            <button
-                                                onClick={() => setShowInteractions(!showInteractions)}
-                                                className={`flex items-center justify-center gap-2 px-3 py-1.5 rounded-md border text-[10px] font-medium transition-all
-                                                    ${showInteractions
-                                                        ? 'bg-green-500/10 border-green-500 text-green-600 dark:text-green-400'
-                                                        : `${isLightMode ? 'bg-white border-neutral-200 text-neutral-600 hover:bg-neutral-50' : 'bg-white/5 border-white/10 text-neutral-400 hover:bg-white/10'}`
-                                                    }`}
-                                                title="Show molecular interactions (H-bonds, salt bridges)"
-                                            >
-                                                <span className={`w-1.5 h-1.5 rounded-full ${showInteractions ? 'bg-green-500' : 'bg-neutral-400'}`} />
-                                                {showInteractions ? 'Interactions On' : 'Interactions Off'}
-                                            </button>
-                                        )}
                                     </div>
                                     <div className="flex flex-wrap gap-1">
                                         {ligands.map(lig => (

src/components/ProteinViewer.tsx

@@ -41,7 +41,6 @@ export interface ProteinViewerProps {
     showSurface: boolean;
     showLigands?: boolean;  // Optional, defaults to true
     showIons?: boolean;     // New prop
-    showInteractions?: boolean; // Show H-bonds and interactions
     coloring: ColoringType;
     palette: ColorPalette;
     backgroundColor: string;
@@ -119,7 +118,6 @@ export const ProteinViewer = forwardRef<ProteinViewerRef, ProteinViewerProps>(({
     showSurface = false,
     showLigands = false,
     showIons = false,
-    showInteractions = false,
     isSpinning = false,
     isMeasurementMode = false,
     measurements,
@@ -1856,72 +1854,9 @@ export const ProteinViewer = forwardRef<ProteinViewerRef, ProteinViewerProps>(({
         }
     };
 
-    // Update Interactions (H-bonds, Salt bridges, Disulfide bonds)
-    const updateInteractions = () => {
-        const component = componentRef.current;
-        if (!component || !showInteractions) {
-            // Remove existing interaction representations
-            if (component) {
-                component.removeRepresentation(component.reprList.filter((r: any) => r.name && r.name.startsWith('interaction_')));
-            }
-            return;
-        }
-
-        try {
-            // Remove old interaction reps
-            component.reprList.filter((r: any) => r.name && r.name.startsWith('interaction_')).forEach((r: any) => component.removeRepresentation(r));
-
-
-            // 1. Hydrogen Bonds (Backbone N-H...O=C)
-            // Using distance representation for atoms within H-bond distance
-            component.addRepresentation('distance', {
-                atomPair: [
-                    ['protein and .N', 'protein and .O'],
-                ],
-                labelVisible: false,
-                color: 'lightblue',
-                linewidth: 1,
-                opacity: 0.6,
-                name: 'interaction_hbond',
-                maxDistance: 3.5,  // Typical H-bond distance
-            });
-
-            // 2. Salt Bridges (Charged residues)
-            // Positive: ARG, LYS; Negative: ASP, GLU
-            component.addRepresentation('distance', {
-                atomPair: [
-                    ['( ARG or LYS ) and ( .NH* or .NZ )', '( ASP or GLU ) and ( .OD* or .OE* )'],
-                ],
-                labelVisible: false,
-                color: 'orange',
-                linewidth: 2,
-                opacity: 0.7,
-                name: 'interaction_saltbridge',
-                maxDistance: 4.0,  // Salt bridge cutoff
-            });
-
-            // 3. Disulfide Bonds (CYS SG-SG)
-            component.addRepresentation('distance', {
-                atomPair: [
-                    ['CYS and .SG', 'CYS and .SG'],
-                ],
-                labelVisible: false,
-                color: 'yellow',
-                linewidth: 3,
-                opacity: 0.9,
-                name: 'interaction_disulfide',
-                maxDistance: 2.5,  // Disulfide bond distance
-            });
-
-        } catch (e) {
-            console.warn("Error adding interactions:", e);
-        }
-    };
-
     useEffect(() => {
         updateRepresentation();
-        updateInteractions();
-    }, [representation, coloring, customColors, showSurface, showLigands, showIons, colorPalette, showInteractions]);
+    }, [representation, coloring, customColors, showSurface, showLigands, showIons, colorPalette]);
 
     useEffect(() => {
         if (stageRef.current) {